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7xsu

Cardiac sodium channel in complex with LqhIII

Method: ELECTRON MICROSCOPY Dmax: 130.7 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Sodium channel protein type 5 subunit alpha,G protein/GFP fusion protein

Recombinant vesicular stomatitis Indiana virus rVSV-G/GFP

UniProt B7UCZ6

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Insufficient information Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain A； UniProt 512–750 Not recorded Alpha-like toxin Lqh3 × 1 （P56678） NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5 BMA beta-D-mannopyranose × 1 6OU [(2~{R})-1-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-3-hexadecanoyloxy-propan-2-yl] (~{Z})-octadec-9-enoate × 6 9Z9 (3beta,14beta,17beta,25R)-3-[4-methoxy-3-(methoxymethyl)butoxy]spirost-5-en × 1 ELECTRON MICROSCOPY cryo-EM buffer：pH 6.1 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 3.40 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 7XSU Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
6ZQO EYFP mutant - F165G Deposited 2020-07-10 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 512–750（239 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；5.7 mg/ml in 20mM Tris 8.0 200 mM NaCl mixed with a 1.44M (NH4)2SO4, 60mM Bicine pH 9.0 reservoir solution.
Resolution 2.20 Å R-free 0.340
7EYE Cryo-EM (SPA) structure of Nup155 N-terminus (19-863) at 5.1 Angstrom resolution Deposited 2021-05-30 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 512–750（239 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；Buffer was freshly made.
cryo-EM vitrification conditions Cryogen ETHANE；Blot for 3 seconds before plunging
Resolution 5.10 Å
7EYQ Cryo-EM (SPA) structure of human Nup155 Longer N-terminus (19-1069) at 5.4 Angstrom resolution Deposited 2021-05-31 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 512–750（239 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；Buffer was freshly made.
cryo-EM vitrification conditions Cryogen ETHANE；Blot for 3 seconds before plunging
Resolution 5.40 Å
7FBS structure of a channel Deposited 2021-07-12 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 512–750（239 aa）
Mutation：I1487Q,F1488Q,M1489Q NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 6OU [(2~{R})-1-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-3-hexadecanoyloxy-propan-2-yl] (~{Z})-octadec-9-enoate × 11 4Y4 1-[2-[(2R)-2-oxidanyl-3-(propylamino)propoxy]phenyl]-3-phenyl-propan-1-one × 1 9Z9 (3beta,14beta,17beta,25R)-3-[4-methoxy-3-(methoxymethyl)butoxy]spirost-5-en × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
9NTM SPEF1 bound to 14-pf microtubule Deposited 2025-03-18 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 89 PDB declaration: 89-meric
Chain 1A 512–750（239 aa）
Chain 1B 512–750（239 aa）
Chain 1C 512–750（239 aa）
Chain 1D 512–750（239 aa）
Chain 1E 512–750（239 aa）
Not recorded GTP GUANOSINE-5'-TRIPHOSPHATE × 42 MG MAGNESIUM ION × 42 GDP GUANOSINE-5'-DIPHOSPHATE × 42 TA1 TAXOL × 42 ELECTRON MICROSCOPY
cryo-EM buffer pH 6.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.10 Å

5 other PDB entries and 5 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name B7UCZ6_9RHAB
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1590–1828； UniProt 512–750

Sodium channel protein type 5 subunit alpha,G protein/GFP fusion protein

Recombinant vesicular stomatitis Indiana virus rVSV-G/GFP

UniProt P15389

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Insufficient information Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain A； UniProt 1–461 Chain A； UniProt 659–1068 Chain A； UniProt 1190–1898 Not recorded Alpha-like toxin Lqh3 × 1 （P56678） NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5 BMA beta-D-mannopyranose × 1 6OU [(2~{R})-1-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-3-hexadecanoyloxy-propan-2-yl] (~{Z})-octadec-9-enoate × 6 9Z9 (3beta,14beta,17beta,25R)-3-[4-methoxy-3-(methoxymethyl)butoxy]spirost-5-en × 1 ELECTRON MICROSCOPY cryo-EM buffer：pH 6.1 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 3.40 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 7XSU Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
6UZ0 Cardiac sodium channel with flecainide Deposited 2019-11-14 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–1898（1898 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 9Z9 (3beta,14beta,17beta,25R)-3-[4-methoxy-3-(methoxymethyl)butoxy]spirost-5-en × 5 6OU [(2~{R})-1-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-3-hexadecanoyloxy-propan-2-yl] (~{Z})-octadec-9-enoate × 11 K4D Flecainide × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 6
cryo-EM vitrification conditions Cryogen ETHANE；waiting for 20s, blot for 2.5-3.5s before plunging
Resolution 3.24 Å
6UZ3 Cardiac sodium channel Deposited 2019-11-14 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–1898（1898 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 9Z9 (3beta,14beta,17beta,25R)-3-[4-methoxy-3-(methoxymethyl)butoxy]spirost-5-en × 5 6OU [(2~{R})-1-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-3-hexadecanoyloxy-propan-2-yl] (~{Z})-octadec-9-enoate × 11 ELECTRON MICROSCOPY
cryo-EM buffer pH 6
cryo-EM vitrification conditions Cryogen ETHANE；waiting for 20s, blot for 2.5-3.5s before plunging
Resolution 3.50 Å
7FBS structure of a channel Deposited 2021-07-12 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–461（461 aa）
Chain A 659–1068（410 aa）
Chain A 1190–1898（709 aa）
Mutation：I1487Q,F1488Q,M1489Q Mutation：I1487Q,F1488Q,M1489Q Mutation：I1487Q,F1488Q,M1489Q NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 6OU [(2~{R})-1-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-3-hexadecanoyloxy-propan-2-yl] (~{Z})-octadec-9-enoate × 11 4Y4 1-[2-[(2R)-2-oxidanyl-3-(propylamino)propoxy]phenyl]-3-phenyl-propan-1-one × 1 9Z9 (3beta,14beta,17beta,25R)-3-[4-methoxy-3-(methoxymethyl)butoxy]spirost-5-en × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
7K18 Cardiac Sodium channel with toxin bound Deposited 2020-09-07 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–1898（1898 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 6OU [(2~{R})-1-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-3-hexadecanoyloxy-propan-2-yl] (~{Z})-octadec-9-enoate × 11 ELECTRON MICROSCOPY
cryo-EM buffer pH 6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
8F6P Rat Cardiac Sodium Channel with Ranolazine Bound Deposited 2022-11-16 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–461（461 aa）
Chain A 659–1068（410 aa）
Chain A 1137–1845（709 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 7 BMA beta-D-mannopyranose × 3 XHO (R)-ranolazine × 1 6OU [(2~{R})-1-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-3-hexadecanoyloxy-propan-2-yl] (~{Z})-octadec-9-enoate × 6 Y01 CHOLESTEROL HEMISUCCINATE × 13 ELECTRON MICROSCOPY
cryo-EM buffer pH 6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
8T6L Cryo-EM structure of rat cardiac sodium channel NaV1.5 with batrachotoxin analog BTX-B Deposited 2023-06-16 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–1931（1931 aa）
Mutation：A33T,G214D NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 LBN 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine × 10 Y01 CHOLESTEROL HEMISUCCINATE × 11 9Z9 (3beta,14beta,17beta,25R)-3-[4-methoxy-3-(methoxymethyl)butoxy]spirost-5-en × 2 YIJ (1R)-1-[(5aR,7aR,9R,11aS,11bS,12R,13aR)-9,12-dihydroxy-2,11a-dimethyl-1,2,3,4,7a,8,9,10,11,11a,12,13-dodecahydro-7H-9,11b-epoxy-13a,5a-prop[1]enophenanthro[2,1-f][1,4]oxazepin-14-yl]ethyl benzoate × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å

6 other PDB entries and 6 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name SCN5A_RAT
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–461； UniProt 1–461 Author chain A； PDBConstruct 462–871； UniProt 659–1068 Author chain A； PDBConstruct 872–1580； UniProt 1190–1898

Alpha-like toxin Lqh3

OrganismNot specified

UniProt P56678

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Insufficient information Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain B； UniProt 1–67 Not recorded Sodium channel protein type 5 subunit alpha,G protein/GFP fusion protein × 1 （P15389,B7UCZ6） NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5 BMA beta-D-mannopyranose × 1 6OU [(2~{R})-1-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-3-hexadecanoyloxy-propan-2-yl] (~{Z})-octadec-9-enoate × 6 9Z9 (3beta,14beta,17beta,25R)-3-[4-methoxy-3-(methoxymethyl)butoxy]spirost-5-en × 1 ELECTRON MICROSCOPY cryo-EM buffer：pH 6.1 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 3.40 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 7XSU Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1BMR ALPHA-LIKE TOXIN LQH III FROM SCORPION LEIURUS QUINQUESTRIATUS HEBRAEUS, NMR, 25 STRUCTURES Deposited 1998-07-24 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–67（67 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 5.8；311 K；Ionic strength (raw mmCIF value) 100 mM PHOSPHATE BUFFER；Pressure 1
NMR sample composition 90% WATER/10% D2O
Resolution not provided
1FH3 NMR STRUCTURES OF LQH III ALPHA-LIKE SCORPION TOXIN FROM LEIURUS QUINQUESTRIATUS CORRESPONDING TO THE MAJOR CONFORMER IN SOLUTION Deposited 2000-07-31 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–67（67 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 5.8；311 K；Ionic strength (raw mmCIF value) NA；Pressure 1
NMR sample composition 2mM LqhIII; 100 mM phosphate buffer pH 5.8; 90% H2O 10% D2O | 90% H2O/10% D2O
Resolution not provided
7K18 Cardiac Sodium channel with toxin bound Deposited 2020-09-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–67（67 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 6OU [(2~{R})-1-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-3-hexadecanoyloxy-propan-2-yl] (~{Z})-octadec-9-enoate × 11 ELECTRON MICROSCOPY
cryo-EM buffer pH 6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å

3 other PDB entries and 3 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name SCL3_LEIHE
Isoform —
PDB entities 2
Chains and sequence ranges Author chain B； PDBConstruct 1–67； UniProt 1–67

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

SAXS profile for 7xsu

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 7xsu
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2. Structure Basics 2. Structure Basics

Entry ID entry_id7xsu
Deposition date deposition_date2022-05-15
Structure title titleCardiac sodium channel in complex with LqhIII
Keywords keywordscardiac sodium channel, MEMBRANE PROTEIN, MEMBRANE PROTEIN-TOXIN complex; MEMBRANE PROTEIN/TOXIN
Experimental Method methodELECTRON MICROSCOPY
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier36.28 Å
Radius of gyration Rg (electron density) rg_electron35.21 Å
Forward intensity I(0) i0211424000.00
Molecular weight molecular_weight127320.0 kDa
Excluded volume excluded_volume163530 ų
Envelope volume envelope_volume222660 ų
Hydration-shell volume shell_volume52613 ų
Envelope diameter envelope_diameter140.6 Å
Shell Rg shell_rg41.48 Å
Envelope Rg envelope_rg35.79 Å
Shape Rg shape_rg35.21 Å
Total Rg total_rg35.67 Å
Total atoms total_atoms8969
Residues n_residues1152
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax130.7 Å
Rg (real space) rg_real36.19 Å
Rg uncertainty (real space) rg_real_error0.94 Å
I(0) (real space) i0_real2.1140e+08
I(0) uncertainty (real space) i0_real_error3.1690e+06
Rg (reciprocal space) rg_reciprocal36.25 Å
I(0) (reciprocal space) i0_reciprocal211400000.0000
Solution quality estimate total_estimate0.8487
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary47.5 Å
Skewness Skewness skewness0.295
Kurtosis Kurtosis kurtosis-0.135
Angular range angular_range— – 0.2200 Å−1
Current regularization parameter α current_alpha0.0002
Highest regularization parameter α highest_alpha23980000.0000
Real-space data points n_real_points45
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.681; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.993; Smooth: 0.993
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (6)

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8. Citations (1)

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9. Files and Curves (10)